crossing96/oncoscreening huggingface dataset:
Prediction of pathological response following neoadjuvant chemotherapy in patients with muscle-invasive bladder cancer: the PRE-PREVENCYS trial.	BACKGROUND: The recommended treatment for patients with non-metastatic muscle-invasive bladder cancer (MIBC) is neoadjuvant chemotherapy (NAC) and radical cystectomy (RC). Following NAC, 20-40% of patients experience a complete pathological response (pCR) in the RC specimen and these patients have excellent long-term overall survival. Subject to debate is, however, whether patients with a pCR to NAC benefit from RC, which is a major surgical procedure with substantial morbidity, and if these patients might be candidates for close surveillance instead. However, currently it is not possible to accurately identify patients with a pCR to NAC in whom RC might be withheld. The objective of this study is to assess whether pathological response in the RC specimen after NAC can be predicted based on clinical, radiological, and histological variables and on a wide set of molecular biomarkers assessed in tissue, blood and urine. METHODS: This is a multicentre, prospective cohort study, including patients with cT2a-T4a N0-N1 M0 urothelial cell MIBC who are scheduled to undergo cisplatin-based NAC followed by RC. Prior to start of therapy, a 2-Deoxy-2-[18F] fluorodeoxyglucose ((18)F-FDG) positron emission tomography/computed tomography (PET/CT) is performed. Response to NAC is evaluated by CT-scan. Blood and urine, including cytology, are prospectively collected for biomarker analyses before and after NAC. Immediately before RC, participants undergo cystoscopy with bimanual examination and a re-staging transurethral resection (TUR) of all visible cancerous lesions or with biopsies from scar tissue. Subsequently, RC is performed in all patients. Tissue from the diagnostic TUR, the re-staging TUR, and the RC specimen is examined for the presence of urothelial cancer carcinoma and DNA and RNA is isolated for molecular analysis. The primary endpoint is the pathological stage (ypTN) in the RC and ePLND specimen and its association with clinical response. DISCUSSION: If the PRE-PREVENCYS trial shows that the absence of residual disease after NAC in patients with MIBC is accurately predicted, a randomized controlled trial is scheduled comparing the overall survival of NAC plus RC versus NAC followed by close surveillance for patients with a clinically complete response (PREVENCYS trial). TRIAL REGISTRATION: Netherlands Trial Register: NL8678; Registered 20 May 2020 https://www.trialregister.nl/trial/8678.	bladder
Defining radical cystectomy using the ICD-10 procedure coding system.	INTRODUCTION: The International Classification of Diseases-10-Procedure Coding System (ICD-10-PCS) is markedly more complex than the preceding ICD-9 system, which has increased the difficulty of identifying radical cystectomy (RC) in administrative datasets. Given the absence of a consensus code definition for RC, we sought to develop and internally validate a list of ICD-10-PCS codes for RC. MATERIALS AND METHODS: All RCs performed from January 2019 to December 2020 were identified from our prospectively maintained registries and split into training (2019) and validation (2020) cohorts. A list of candidate ICD-10-PCS codes to identify RC were compiled using an online ICD-9 to ICD-10 converter. Codes were used to identify RCs from hospital billing data and referenced against registry cases in the training cohort; when discrepancies were found, the working ICD-10 code definition was iteratively revised. Accuracy of the consensus code list was verified in the validation cohort. RESULTS: We identified 459 RCs over the study period, including 225 in 2019 and 234 in 2020. In the training cohort, our codes identified 241 procedures, including 222 of 225 (99%) RCs performed for bladder cancer. Misidentified cases included 15 (6.2%) RCs for benign disease or nonurologic cancers and 4 (1.7%) non-RC cases. In the validation cohort we identified 239 cases, including 227 of 234 (97%) RCs for bladder cancer and 12 (5%) RCs for benign disease or nonurologic cancers. CONCLUSION: Given high fidelity to actual procedures performed, this list of ICD-10-PCS codes may be useful for researchers seeking to identify RC within administrative datasets.	bladder
Intracorporeal Versus Extracorporeal Neobladder After Robot-assisted Radical Cystectomy: Results From the International Robotic Cystectomy Consortium.	OBJECTIVE: To compare perioperative and oncologic outcomes of intracorporeal (ICNB) and extracorporeal neobladder (ECNB) following robot assisted radical cystectomy (RARC) from a multi-institutional, prospectively maintained database, the International Robotic Cystectomy Consortium (IRCC). METHODS: A retrospective review of IRCC database between 2003 and 2020 (3742 patients from 33 institutions across 14 countries) was performed (I-79606). The Cochran-Armitage trend test was used to assess utilization of ICNB over time. Multivariate logistic regression models were fit to evaluate variables associated with receiving ICNB, overall complications, high-grade complications, and readmissions after RARC. Kaplan Meier curves were used to depict recurrence-free, disease-specific, and overall survival. RESULTS: Four hundred eleven patients received neobladder, 64% underwent ICNB. ICNB utilization increased significantly over time (P <.01). Patients who received ICNB were readmitted and received neoadjuvant chemotherapy more frequently (36% vs 24%, P = .03, 35% vs 8%, P <.01, respectively). ICNB was associated with older age (OR 1.04, 95% CI 1.01-1.07, P = .001), receipt of neoadjuvant chemotherapy (OR 4.63, 95% CI 2.34-9.18, P <.01), and more recent RARC era (2016-2020) (OR 12.6, 95% CI 5.6-28.4, P <.01). On multivariate analysis, ICNB (OR 5.43, 95% CI 2.34-12.58, P <.01), positive surgical margin (OR 4.88, 95% CI 1.29-18.42, P = .019), longer operative times (OR 1.26, 95% CI 1.00-1.58, P = .048), and institutional annual RARC volume (OR 1.09, 95% CI 1.05-1.12, P <.01) were associated with readmissions. CONCLUSION: Utilization of ICNB increased significantly over time. Patients who underwent RARC and ICNB had shorter hospital stays and fewer 30-d reoperations but were readmitted more frequently compared to those who underwent ECNB.	bladder
The feasibility of reduced field-of-view diffusion-weighted imaging in evaluating bladder invasion of uterine cervical cancer.	OBJECTIVES: Uterine cervical cancer with bladder mucosal invasion is classified as FIGO stage IVA with poor prognosis. MRI can rule out the bladder invasion and skipping cystoscopy may be possible; however, high false-positive rate may be problematic. The purpose of this study is to evaluate the diagnostic performance of reduced field-of-view (FOV) diffusion-weighted imaging (DWI) in evaluating bladder mucosal invasion of cervical cancer. METHODS: 3T MRI including T2WI and reduced FOV DWI in 15 women with histologically proven cervical cancer (two stage IIIB, six stage IVA, seven stage IVB) were retrospectively evaluated compared with cystoscopic findings. RESULTS: Cystoscopy revealed mucosal invasion in 13 of 15 cases. The border between the tumor and the bladder wall was unclear on T2WI and clear on reduced FOV DWI in all 15 cases. The diagnosis of mucosal invasion on reduced FOV DWI had a sensitivity of 100%, specificity of 50%, accuracy of 93%, PPV of 93%, and NPV of 100%. CONCLUSIONS: Addition of reduced FOV DWI may improve the staging accuracy of MRI for cervical cancer in assessing the bladder mucosal invasion. ADVANCES IN KNOWLEDGE: Reduced FOV DWI may improve the staging accuracy of cervical cancer in assessing bladder mucosal invasion with high NPV and PPV, which may be helpful for avoiding unnecessary cystoscopy.	bladder
A Retrospective Analysis of Clinical and Pathologic Characteristics of Recurrent Bladder Tumor in a Tertiary Hospital in Addis Ababa, Ethiopia.	BACKGROUND: Previous recurrences, tumor category (Ta, T1), the presence of CIS with superficial bladder tumors, the number of tumors, tumor size and multiplicity are predictors of bladder tumor recurrence. Recurrence is better predicted by multiplicity, size and previous recurrence. METHODS: This is retrospective descriptive study. All patients with urinary bladder tumor admitted to TASH from January 1st, 2018 to December 31st, 2019 is the study population. Information was retrieved using structured questionnaire. RESULTS: Most of the recurrent tumors 55 (76.4%) had huge size and were multiple 62 (86.1%) in the primary presentation. Most recurrent tumors 47 (65.3%) are low grade bladder tumors. About 17 (23.6%) were high grade tumor in their primary presentation. European studies showed size and multiplicity increase risk of recurrence. However, our patients have late presentations which probably made the proportion of recurrence higher. CONCLUSION: Most of the recurrent bladder tumors have huge size and multiple in number at their initial presentation. All histological variants of Urothelial carcinomas recur.	bladder
LINC00958 promotes bladder cancer carcinogenesis by targeting miR-490-3p and AURKA.	BACKGROUND: Bladder cancer is a prevalent malignancy of the urinary system, in which long non-coding RNAs (lncRNAs) are highly associated. We aimed to elucidate the role of LINC00958 in bladder cancer. METHODS: LINC00958 expression levels were measured using qRT-PCR. The interaction of LINC00958-miR-490-3p-AURKA was analyzed by luciferase, RIP, and RNA pull-down assays. The biological roles of LINC00958, miR-490-3p, and AURKA in bladder cancer cells were analyzed using CCK8, BrdU, and transwell assays. RESULTS: Increased expression of LINC00958 and AURKA was observed in bladder cancer tissues and cell lines. Decreased LINC00958 expression repressed bladder cancer progression and downregulation of miR-490-3p accelerated bladder cancer cell progression. Moreover, LINC00958 sponges miR-490-3p to upregulate AURKA expression, thereby promoting carcinogenesis in bladder cancer cells. CONCLUSIONS: Our study revealed that LINC00958 facilitated cell proliferation and invasion, and suppressed cell apoptosis by sponging miR-490-3p and upregulating AURKA, thus inspiring a new treatment method for bladder cancer.	bladder
Impact of C-reactive Protein Flare Response in Patients With Advanced Urothelial Carcinoma Who Received Pembrolizumab.	BACKGROUND/AIM: To clarify the clinical significance of the temporary elevated C-reactive protein (CRP) levels followed by a decrease below baseline (CRP flare response) after administration of pembrolizumab to patients with advanced urothelial carcinoma (UC). PATIENTS AND METHODS: We retrospectively reviewed 31 patients with advanced UC who received pembrolizumab. Patients were categorized into 3 groups (flare-responder, responder, non-responder) according to early CRP kinetics. Intergroup tumor response and survivals were compared. RESULTS: Objective response rates of flare-responder, responder, and non-responder groups were 75%, 80%, and 26%, respectively. Median overall survival was not reached in flare-responder and responder groups, and was 10.2 months in the non-responder group (p=0.03). Furthermore, the flare-responder group did not reach median progression-free survival, and for the responder and non-responder groups it was 15.2 and 2.8 months, respectively (p=0.03). CONCLUSION: CRP flare response might be a promising biomarker in patients with advanced UC who received pembrolizumab.	bladder
Infrared molecular fingerprinting of blood-based liquid biopsies for the detection of cancer.	Recent omics analyses of human biofluids provide opportunities to probe selected species of biomolecules for disease diagnostics. Fourier-transform infrared (FTIR) spectroscopy investigates the full repertoire of molecular species within a sample at once. Here, we present a multi-institutional study in which we analysed infrared fingerprints of plasma and serum samples from 1639 individuals with different solid tumours and carefully matched symptomatic and non-symptomatic reference individuals. Focusing on breast, bladder, prostate, and lung cancer, we find that infrared molecular fingerprinting is capable of detecting cancer: training a support vector machine algorithm allowed us to obtain binary classification performance in the range of 0.78-0.89 (area under the receiver operating characteristic curve [AUC]), with a clear correlation between AUC and tumour load. Intriguingly, we find that the spectral signatures differ between different cancer types. This study lays the foundation for high-throughput onco-IR-phenotyping of four common cancers, providing a cost-effective, complementary analytical tool for disease recognition.	bladder
[Clinical pathological expert consensus on HER-2 testing in urothelial carcinoma in China].	Human epidermal growth factor receptor 2 (HER-2) plays an important role in carcinogenesis and development of urothelial carcinoma. Overexpression of HER-2 is associated with poor prognosis of urothelial carcinoma. Although there is no significant benefit from anti-HER-2 targeted therapies of monoclonal antibody and tyrosine kinase inhibitor, Anti-HER-2 antibody-drug conjugate (HER-2-ADC) has shown a promising efficacy in urothelial carcinoma patients with HER-2 overexpression. Therefore, effectively screening the potential beneficiaries of HER-2-ADC drugs has become a new challenge. However, standardized HER-2 scoring system for urothelial carcinoma has yet to be developed. Thus, the Committees organized experts to reach this expert consensus based on the clinical practice of HER-2 expression, gene amplification and mutation testing in urothelial carcinoma, combined with the current research progress and internal discussion of committee members, in order to construct HER-2 testing standard of urothelial carcinoma and improve the accuracy of interpretation, to guide the clinical application.	bladder
Cost-Effectiveness of Avelumab Maintenance Therapy for Advanced or Metastatic Urothelial Carcinoma in the United States.	INTRODUCTION: The JAVELIN Bladder 100 trial showed that maintenance avelumab therapy after chemotherapy improved the survival of patients with advanced or metastatic urothelial carcinoma. We analyzed the cost-effectiveness of maintenance therapy with avelumab plus best supportive care (BSC) in patients with advanced or metastatic urothelial carcinoma after receiving first-line platinum-based chemotherapy from the US payer perspective. METHODS: A Markov model was used to analyze the economic outcomes of maintenance avelumab plus BSC (avelumab strategy) in the treatment of urothelial carcinoma. The clinical data were derived from the JAVELIN Bladder 100 trial. All cost information was obtained from Medicare and published literature. The total cost, total life years (LYs), total quality-adjusted LYs (QALYs), incremental cost-effectiveness ratio (ICER), and incremental net health benefit (INHB) were calculated. One-way sensitivity analysis and probabilistic sensitivity analysis were also performed. RESULTS: Our results showed that avelumab strategy versus BSC strategy cost US $176,352 and $238,661 and yielded an additional 0.465 and 1.007 QALY in all patients with unknown programmed-death ligand 1 (PD-L1) status and the PD-L1-positive subpopulation, respectively, which led to an ICER of $102,365/QALY and $106,253/QALY gained. In all patients with unknown PD-L1 status, maintenance avelumab plus BSC therapy guiding by PD-L1 expression testing (PD-L1-guided strategy) compared with the avelumab strategy and BSC strategy resulted in ICER of $105,360/QALY and $122,653/QALY, respectively. The probabilities of the avelumab strategy and the PD-L1-guided strategy being cost-effective in the simultaneous competition of the three strategies were 38.49% and 48.82%. In patients with PD-L1-positive status, the avelumab strategy had an 87.51% probability of cost-effectiveness. The most influential parameter for the model was the cost of avelumab and pembrolizumab. CONCLUSIONS: This analysis demonstrated that maintenance therapy with avelumab plus BSC may be a cost-effective option for patients with advanced or metastatic urothelial carcinoma at a willingness-to-pay (WTP) threshold of $150,000/QALY, especially for patients with PD-L1-positive status.	bladder
Investigation of the relationship between MMP-1 (- 1607 1G/2G), MMP-3 (- 1171 5A/6A) gene variations and development of bladder cancer.	BACKGROUND: Chronic inflammation is an important risk factor in the development of bladder cancer. It may stimulate growth and metastasis of cancer cells. The inflammatory process includes MMP activities and expression. MMP activation can be stimulated by various inflammatory cells. Pathological processes such as bladder cancer may occur due to imbalance in MMP activities. In our study, we aimed to determine the relationship between MMP-1, MMP-3 gene variations associated with chronic inflammation and the bladder cancer development. METHODS: Our study was carried out with 89 bladder cancer patients and 78 healthy controls. PCR-RFLP methods were applied to determine MMP-1 and MMP-3 gene variations genotype distributions. RESULTS: 1G/1G homozygous and 1G/2G heterozygous genotypes of MMP-1 gene variation were determined more in patients than controls. The 5A/5A homozygous and 5A/6A heterozygous genotypes of the MMP-3 gene variation were detected more in patients than controls. The significant difference was detected in terms of genotype distributions of MMP-1 and MMP-3 gene variations between these groups (p < 0.05). In addition to, the most common haplotype in the patient group were detected as 1G/2G-5A/6A (20.22%). CONCLUSION: In this study, MMP-1 and MMP-3 gene variations were determined as possible genetic risk factors for bladder cancer development in the Thrace population.	bladder
Incidence, Etiology, Prevention and Management of Ureteroenteric Strictures after Robot-Assisted Radical Cystectomy: A Review of Published Evidence and Personal Experience.	Benign ureteroenteric anastomosis strictures (UESs) are one of many critical complications that may cause irreversible disability following robot-assisted radical cystectomy (RARC). Previous studies have shown that the incidence rates of UES after RARC can reach 25.3%, with RARC having higher UES incidence rates compared to open radical cystectomy. Various known and unknown factors are involved in the occurrence of UES. To minimize the incidence of UES after RARC, our group has standardized the procedure and technique for intracorporeal urinary diversion by applying the following five strategies: (1) wide delicate dissection of the ureter and preservation of the periureteral tissues; (2) gentle handling of the ureter and security of periureteral tissues at the anastomotic site; (3) use of indocyanine green to confirm good blood supply; (4) standardization of the ample ureteral spatulation length for Wallace ureteroenteric anastomosis through objective measurements; and (5) development of an institutional standardized procedure manual. This review focused on the incidence, etiology, prevention, and management of UES after RARC to bring attention to the incidence of this complication while also proposing standardized surgical procedures to minimize its incidence after RARC.	bladder
A novel self-learning framework for bladder cancer grading using histopathological images.	In recent times, bladder cancer has increased significantly in terms of incidence and mortality. Currently, two subtypes are known based on tumour growth: non-muscle invasive (NMIBC) and muscle-invasive bladder cancer (MIBC). In this work, we focus on the MIBC subtype because it has the worst prognosis and can spread to adjacent organs. We present a self-learning framework to grade bladder cancer from histological images stained by immunohistochemical techniques. Specifically, we propose a novel Deep Convolutional Embedded Attention Clustering (DCEAC) which allows for the classification of histological patches into different levels of disease severity, according to established patterns in the literature. The proposed DCEAC model follows a fully unsupervised two-step learning methodology to discern between non-tumour, mild and infiltrative patterns from high-resolution 512 × 512 pixel samples. Our system outperforms previous clustering-based methods by including a convolutional attention module, which enables the refinement of the features of the latent space prior to the classification stage. The proposed network surpasses state-of-the-art approaches by 2-3% across different metrics, reaching a final average accuracy of 0.9034 in a multi-class scenario. Furthermore, the reported class activation maps evidence that our model is able to learn by itself the same patterns that clinicians consider relevant, without requiring previous annotation steps. This represents a breakthrough in MIBC grading that bridges the gap with respect to training the model on labelled data.	bladder
Genetic variants in splicing factor genes and susceptibility to bladder cancer.	BACKGROUND: Genome-wide association studies have demonstrated that genetic variants are closely related to tumorigenesis and progression of cancer. However, the correlation between genetic variants in splicing factor genes and bladder cancer susceptibility remains unclear. METHOD: A case-control study with 580 cases of bladder cancer and 1,101 controls was conducted to explore the association of single-nucleotide polymorphisms (SNPs) in splicing factors with bladder cancer susceptibility by logistic regression models, and multiple testing errors were justified by the false discovery rate (FDR) method. Next, we used the Cancer Genome Atlas (TCGA) database and the Gene Expression Omnibus (GEO) datasets to further analyze the differential expression of candidate genes. RESULTS: We found that rs978416 G>A in RBFOX3 contributed to a reduced risk of bladder cancer [adjusted odds ratio (OR) = 0.72, 95% confidence internal (CI) = 0.62-0.84, P = 3.54 × 10(-5)], especially in individuals who never smoked (P = 7.83 × 10(-5)). Stratified analysis showed that the protective effect of rs978416 was more significant in the subgroup of low grade and non-muscle invasive bladder cancer. Furthermore, the RBFOX3 mRNA expression was decreased in bladder tumor tissues. However, the relatively high expression of RBFOX3 was related to a higher bladder cancer stage. CONCLUSIONS: Our findings indicated that SNP rs978416 G>A in RBFOX3 may be related to bladder cancer predisposition in Chinese population and might serve as a novel biomarker for bladder cancer risk.	bladder
Bicyclic Peptide Makes Targeting EphA2 Possible.	A tumor-penetrating bicyclic peptide that delivers a toxic payload may have finally unlocked the therapeutic potential of targeting EphA2. According to phase I trial data, BT5528 yielded clinical responses in three patients with ovarian and urothelial cancers-without any of the toxicity issues that have plagued other EphA2-directed therapeutic candidates.	bladder